Sains Malaysiana 47(12)(2018): 2941–2950

http://dx.doi.org/10.17576/jsm-2018-4712-02

Identification of Sequence Motifs for the Protein Components of Type IX Secretion System

(Pengenalpastian Motif Jujukan bagi Komponen Protein Sistem Perembesan Jenis IX)

REEKI EMRIZAL & NOR AZLAN NOR MUHAMMAD*

Centre for Bioinformatics Research, Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor Darul Ehsan, Malaysia

Received: 30 May 2018/Accepted: 14 September 2018

ABSTRACT

Porphyromonas gingivalis is the bacterium responsible for chronic periodontitis, a severe periodontal disease. Virulence factors produced by this bacterium are secreted by the Type IX Secretion System (T9SS). The specific functions for each protein component of the T9SS have yet to be characterized thus limiting our understanding of the mechanisms associated with the translocation and modification processes of the T9SS. This study aims to identify the sequence motifs for each T9SS component and predict the functions associated with each discovered motif using motif comparisons. We extracted the sequences of 20 T9SS components from the P. gingivalis proteome that were experimentally identified to be important for T9SS function and used them for homology searching against fully sequenced bacterial proteomes. We developed a rigorous pipeline for the identification of seed sequences for each protein family of T9SS components. We verified that each selected seed sequence are true members of the protein family hence sharing conserved sequence motifs using profile Hidden Markov Models. The motifs for each T9SS component are identified and compared to motifs in the Pfam database. The discovered motifs for 11 components with known functions matched the motifs associated with the reported functions. We also suggested the putative functions for four components. PorM and PorW might form the putative energy transduction complex. PorP and PorT might be the putative O-deacylases. The identified motifs for five components matched the motifs associated with functions that related/unrelated to the T9SS.

Keywords: Motifs; periodontal disease; type IX secretion System (T9SS)

ABSTRAK

Porphyromonas gingivalis ialah bakteria yang menyebabkan periodontitis kronik, sejenis penyakit periodontium yang parah. Faktor kevirulenan yang dihasilkan oleh bakteria ini dirembeskan oleh Sistem Perembesan Jenis IX (T9SS). Fungsi khusus bagi setiap komponen protein T9SS masih belum dicirikan menyebabkan pemahaman mengenai proses translokasi dan pengubahsuaian protein oleh T9SS adalah terhad. Kajian ini bertujuan untuk mengenal pasti motif untuk setiap komponen dan meramal fungsi yang boleh dikaitkan dengan motif tersebut menggunakan kaedah perbandingan motif. Jujukan untuk 20 komponen penting T9SS yang dikenal pasti melalui uji kaji diperoleh daripada proteom P. gingivalis. Ia digunakan untuk pencarian homologi terhadap proteom bakteria yang mempunyai jujukan genom yang lengkap. Proses analisis yang rapi telah dihasilkan untuk pengenalpastian jujukan benih bagi setiap famili protein komponen T9SS. Jujukan benih yang dipilih disahkan sebagai ahli sebenar famili protein tersebut justeru berkongsi motif terpelihara menggunakan profil Hidden Markov Models. Motif untuk setiap komponen telah dikenal pasti dan dibandingkan dengan motif daripada pangkalan data Pfam. Motif untuk 11 komponen yang telah diketahui fungsinya dipadankan dengan motif yang dikaitkan dengan fungsi tersebut. Kami turut mencadangkan fungsi putatif untuk empat komponen. PorM dan PorW berkemungkinan membentuk kompleks transduksi tenaga. PorP dan PorT berkemungkinan merupakan O-deasilase. Motif yang dikenal pasti untuk lima komponen padan dengan motif yang dikaitkan dengan fungsi berkaitan/tidak berkaitan dengan T9SS.

Kata kunci: Motif; penyakit periodontium; sistem perembesan jenis IX (T9SS)

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*Corresponding author; email: norazlannm@ukm.edu.my